DOI: 10.1101/498147Dec 16, 2018Paper

Martini bead form factors for nucleic-acids and their application in the refinement of protein/nucleic-acid complexes against SAXS data

BioRxiv : the Preprint Server for Biology
Cristina PaissoniCarlo Camilloni


Small-angle X-ray scattering (SAXS) use in combination with molecular dynamics simulation is hampered by its heavy computational cost. The calculation of SAXS from atomic structures can be speed up by using a coarse grain representation of the structure. Here following the work of Niebling, et al. (J. Appl. Cryst., (2014), 47, 1190) we derived the Martini beads form factors for nucleic acids and we implemented them, together with those previously determined for proteins, in the publicly available PLUMED library. We also implemented a hybrid multi-resolution strategy to perform SAXS restrained simulations at atomic resolution by calculating on-the-fly the virtual position of the Martini beads and using them for the calculation of SAXS. The accuracy and efficiency of the method is demonstrated by refining the structure of two protein/nucleic acid complexes. Instrumental for this result is the use of metainference that allows considering and alleviating the approximations at play in our SAXS calculation.

Related Concepts

Nucleic Acids
Small Molecule Libraries
Nucleic acid binding protein
Positioning Attribute
Small Angle X Ray Scattering

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